Wald Tests

Light(Ab) vs Control(WT)

Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):

## [1] 543

Is A-Beta-Cry2-mCh significantly differentially expressed?:

baseMean log2FoldChange lfcSE stat pvalue padj gene_biotype external_gene_name
A-Beta-Cry2-mCh 326.8102 0.1830931 0.4401487 0.41598 0.6774246 0.8994422 NA NA

## 
##    N   U1   U2   U3   D3   D2   D1 
## 9327  128   80   70   64   77  124

Wnt(Wg) vs. Control(WT)

Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):

## [1] 1049

Is A-Beta-Cry2-mCh significantly differentially expressed?:

baseMean log2FoldChange lfcSE stat pvalue padj gene_biotype external_gene_name
A-Beta-Cry2-mCh 326.8102 -10.75238 1.256863 -8.554939 0 0 NA NA

## 
##    N   U1   U2   U3   D3   D2   D1 
## 8817  365  100   56   82  122  324

Wnt_Light(Wg_Ab) vs. Control(WT)

Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):

## [1] 1068

Is A-Beta-Cry2-mCh significantly differentially expressed?:

baseMean log2FoldChange lfcSE stat pvalue padj gene_biotype external_gene_name
A-Beta-Cry2-mCh 326.8102 1.252949 0.4911453 2.551075 0.0107391 0.0724138 NA NA

## 
##    N   U1   U2   U3   D3   D2   D1 
## 8800  345  106   68   81  127  341

Wnt(Wg) vs. Light(Ab)

Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):

## [1] 996

Is A-Beta-Cry2-mCh significantly differentially expressed?:

baseMean log2FoldChange lfcSE stat pvalue padj gene_biotype external_gene_name
A-Beta-Cry2-mCh 326.8102 -10.93548 1.256597 -8.702451 0 0 NA NA

## 
##    N   U1   U2   U3   D3   D2   D1 
## 8870  296   99   50   88  135  328

Wnt_Light(Wg_Ab) vs Light(Ab)

Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):

## [1] 1118

Is A-Beta-Cry2-mCh significantly differentially expressed?:

baseMean log2FoldChange lfcSE stat pvalue padj gene_biotype external_gene_name
A-Beta-Cry2-mCh 326.8102 1.069856 0.4904657 2.181306 0.0291608 0.1326898 NA NA

## 
##    N   U1   U2   U3   D3   D2   D1 
## 8751  290  120   62  138  177  331

Wnt_Light(Wg_Ab) vs. Wnt(Wg)

Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):

## [1] 178

Is A-Beta-Cry2-mCh significantly differentially expressed?:

baseMean log2FoldChange lfcSE stat pvalue padj gene_biotype external_gene_name
A-Beta-Cry2-mCh 326.8102 12.00533 1.275355 9.413327 0 0 NA NA

## 
##    N   U1   U2   U3   D3   D2   D1 
## 9690   76   22   12   12   20   36

Likelihood Ratio Test

Number of significant genes (padj < 0.1):

## [1] 2801

Session Info

## R version 4.0.5 (2021-03-31)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
##  [1] grid      parallel  stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] forcats_0.5.1               stringr_1.4.0              
##  [3] dplyr_1.0.5                 purrr_0.3.4                
##  [5] readr_1.4.0                 tidyr_1.1.3                
##  [7] tibble_3.1.0                tidyverse_1.3.0            
##  [9] limma_3.46.0                geneplotter_1.68.0         
## [11] annotate_1.68.0             XML_3.99-0.6               
## [13] reshape_0.8.8               lattice_0.20-41            
## [15] ggplot2_3.3.3               gridExtra_2.3              
## [17] biomaRt_2.46.3              gplots_3.1.1               
## [19] RColorBrewer_1.1-2          GenomicFeatures_1.42.3     
## [21] AnnotationDbi_1.52.0        knitr_1.31                 
## [23] DESeq2_1.30.1               SummarizedExperiment_1.20.0
## [25] Biobase_2.50.0              MatrixGenerics_1.2.1       
## [27] matrixStats_0.58.0          GenomicRanges_1.42.0       
## [29] GenomeInfoDb_1.26.7         IRanges_2.24.1             
## [31] S4Vectors_0.28.1            BiocGenerics_0.36.0        
## 
## loaded via a namespace (and not attached):
##  [1] colorspace_2.0-0         ellipsis_0.3.1           rprojroot_2.0.2         
##  [4] XVector_0.30.0           fs_1.5.0                 rstudioapi_0.13         
##  [7] farver_2.1.0             bit64_4.0.5              fansi_0.4.2             
## [10] lubridate_1.7.10         xml2_1.3.2               splines_4.0.5           
## [13] cachem_1.0.4             jsonlite_1.7.2           Rsamtools_2.6.0         
## [16] broom_0.7.6              dbplyr_2.1.1             compiler_4.0.5          
## [19] httr_1.4.2               backports_1.2.1          assertthat_0.2.1        
## [22] Matrix_1.3-2             fastmap_1.1.0            cli_2.4.0               
## [25] htmltools_0.5.1.1        prettyunits_1.1.1        tools_4.0.5             
## [28] gtable_0.3.0             glue_1.4.2               GenomeInfoDbData_1.2.4  
## [31] rappdirs_0.3.3           Rcpp_1.0.6               cellranger_1.1.0        
## [34] jquerylib_0.1.3          vctrs_0.3.7              Biostrings_2.58.0       
## [37] rtracklayer_1.50.0       xfun_0.22                rvest_1.0.0             
## [40] lifecycle_1.0.0          gtools_3.8.2             zlibbioc_1.36.0         
## [43] scales_1.1.1             hms_1.0.0                yaml_2.2.1              
## [46] curl_4.3                 memoise_2.0.0            sass_0.3.1              
## [49] stringi_1.5.3            RSQLite_2.2.6            highr_0.8               
## [52] genefilter_1.72.1        caTools_1.18.2           BiocParallel_1.24.1     
## [55] rlang_0.4.10             pkgconfig_2.0.3          bitops_1.0-6            
## [58] evaluate_0.14            labeling_0.4.2           GenomicAlignments_1.26.0
## [61] bit_4.0.4                tidyselect_1.1.0         plyr_1.8.6              
## [64] magrittr_2.0.1           R6_2.5.0                 generics_0.1.0          
## [67] DelayedArray_0.16.3      DBI_1.1.1                pillar_1.6.0            
## [70] haven_2.3.1              withr_2.4.1              survival_3.2-10         
## [73] RCurl_1.98-1.3           modelr_0.1.8             crayon_1.4.1            
## [76] KernSmooth_2.23-18       utf8_1.2.1               BiocFileCache_1.14.0    
## [79] rmarkdown_2.7            progress_1.2.2           locfit_1.5-9.4          
## [82] readxl_1.3.1             blob_1.2.1               reprex_2.0.0            
## [85] digest_0.6.27            xtable_1.8-4             openssl_1.4.3           
## [88] munsell_0.5.0            bslib_0.2.4              askpass_1.1